Sparse bayesian step-filtering for high-throughput analysis of molecular machine dynamics

ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings

Volumn , Issue , 2010, Pages 4162-4165

  Little, Max A ^a   Jones, Nick S ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Bayes theorem; Convex optimization; Digital filter; L1 regularization; Molecular machines

Indexed keywords

BANDPASS FILTERS; DIGITAL FILTERS; DYNAMICS; SIGNAL PROCESSING; TIME SERIES;

BAYE'S THEOREM; CONVEX OPTIMISATION; FLAGELLAR MOTORS; HIGH-THROUGHPUT ANALYSIS; KINESINS; L1 REGULARIZATIONS; MACHINE DYNAMICS; MOLECULAR MACHINES; SPARSE BAYESIAN; TIMES SERIES;

CONVEX OPTIMIZATION;

EID: 78049391561     PISSN: 15206149     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICASSP.2010.5495722     Document Type: Conference Paper

References (14)

1. P. C. Nelson, M. Radosavljevic, and S. Bromberg, Biological physics : energy, information, life. New York: W.H. Freeman and Co., 2004.
2. P. R. Selvin and T. Ha, Single-molecule techniques : a laboratory manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2008.
3. Y. Sowa, A. D. Rowe, M. C. Leake, T. Yakushi, M. Homma, A. Ishijima, and R. M. Berry, "Direct observation of steps in rotation of the bacterial flagellar motor," Nature, vol. 437, pp. 916-919, 2005.
4. B. C. Carter, M. Vershinin, and S. P. Gross, "A comparison of step-detection methods: How well can you do?," Biophysical Journal, vol. 94, pp. 306-319, 2008.
5. S. H. Chung and R. A. Kennedy, "Forward-Backward Nonlinear Filtering Technique for Extracting Small Biological Signals from Noise," Journal of Neuroscience Methods, vol. 40, pp. 71-86, 1991.
6. B. Kalafut and K. Visscher, "An objective, model-independent method for detection of non-uniform steps in noisy signals," Computer Physics Communications, vol. 179, pp. 716-723, 2008.
7. J. W. J. Kerssemakers, E. L. Munteanu, L. Laan, T. L. Noetzel, M. E. Janson, and M. Dogterom, "Assembly dynamics of microtubules at molecular resolution," Nature, vol. 442, pp. 709-712, 2006.
8. S. A. McKinney, C. Joo, and T. Ha, "Analysis of single-molecule FRET trajectories using hidden Markov modeling," Biophysical Journal, vol. 91, pp. 1941-1951, 2006.
9. G. R. Arce, Nonlinear signal processing : a statistical approach. Hoboken, N.J.: Wiley-Interscience, 2005.
10. S. P. Boyd and L. Vandenberghe, Convex optimization. Cambridge, UK ; New York: Cambridge University Press, 2004.
11. W. H. Press, S. A. Tueukolsky, W. T. Vetterling, and B. P. Flannery, Numerical recipes in C, 2nd ed. Cambridge: Cambridge University Press, 1993.
12. R. Tibshirani, M. Saunders, S. Rosset, J. Zhu, and K. Knight, "Sparsity and smoothness via the fused lasso," Journal of the Royal Statistical Society Series B-Statistical Methodology, vol. 67, pp. 91-108, 2005.
13. S. J. Kim, K. Koh, S. Boyd, and D. Gorinevsky, "l(1) Trend Filtering," Siam Review, vol. 51, pp. 339-360, 2009.
14. T. Pilizota, M. T. Brown, M. C. Leake, R. W. Branch, R. M. Berry, and J. P. Armitage, "A molecular brake, not a clutch, stops the Rhodobacter sphaeroides flagellar motor," Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 11582-11587, 2009.